Genome-Wide Association Study of Nitrogen Use Efficiency Traits in Nigerian Maize Germplasm

This study conducts a genome-wide association study for nitrogen use efficiency traits in a diverse panel of Nigerian maize germplasm, identifying SNP markers associated with NUE components and providing an original genomic resource for NUE improvement breeding. Low nitrogen use efficiency in Nigerian smallholder maize production results in both economic losses from wasted fertiliser investment and environmental damage from nitrogen pollution. Developing maize varieties with genetically improved NUE is a priority for sustainable intensification, but the genetic architecture of NUE in tropical African maize germplasm relevant to Nigeria is incompletely characterised. This study phenotypes 300 diverse maize accessions including Nigerian open-pollinated varieties, early generation hybrids, improved IITA lines, and farmer landraces for NUE component traits including nitrogen uptake efficiency, nitrogen utilisation efficiency, yield under low nitrogen, nitrogen responsiveness under high nitrogen, and root morphology related to nitrogen foraging. Phenotyping is conducted across three environments in Ibadan, Kano, and Benue under low and high nitrogen treatments. Genotyping uses the 600K Affymetrix SNP array. Mixed model GWAS analysis with population structure correction using Q and K model is applied. Findings reveal 47 significant SNP associations (FDR < 0.05) for NUE component traits distributed across 10 chromosomes. Novel significant associations are detected for nitrogen remobilisation efficiency on chromosome 5 and root angle for nitrogen foraging on chromosome 8. Candidate gene analysis identifies nitrate transporters and glutamine synthetase genes in high-linkage disequilibrium with top associations. The study contributes an original GWAS resource for Nigerian maize NUE and recommends marker-assisted selection for the most significant NUE loci. Keywords: GWAS, nitrogen use efficiency, maize germplasm, Nigeria, SNP markers.